Palles Claire, Johnson Nichola, Coupland Ben, Taylor Claire, Carvajal Jaime, Holly Jeff, Fentiman Ian S, Silva Isabel dos Santos, Ashworth Alan, Peto Julian, Fletcher Olivia
Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London SW3 6JB, UK.
Hum Mol Genet. 2008 May 15;17(10):1457-64. doi: 10.1093/hmg/ddn034. Epub 2008 Feb 4.
An important class of genetic variants that affect disease susceptibility may lie within regulatory elements that influence gene expression. Regulatory sequences are difficult to identify and may be distant from the genes they regulate, but many lie within evolutionarily conserved regions (ECRs). We used comparative genomics to identify 12 ECRs up to 75 kb 5' to and within introns of IGF1. These were screened by high-resolution melting curve analysis, and 18 single-nucleotide polymorphisms (SNPs) were identified, including five novel variants. We analysed two large population-based series of healthy women to test the nine SNPs with minor allele frequency (MAF) >1% within ECRs. Three of the nine SNPs within ECRs (rs35455143, rs35765817 and rs3839984) were significantly associated with circulating IGF1 levels in a multivariate analysis (P <or= 0.02 for each SNP, overall significance P < 0.001). All three are uncommon SNPs (MAF <or= 10%) that lie >70 kb 5' of IGF1. Two (rs35455143 and rs35765817) are in strong LD with each other and appear to have opposite effects on circulating IGF1. Our results on a subset of other SNPs in or near IGF1 were consistent with previously reported associations with IGF1 levels, although only one (rs35767: P = 0.05) was statistically significant. We believe that this is the first systematic study of an association between a phenotype and SNPs within ECRs extending over a large region adjacent to a gene. Targeting ECRs appears to be a useful strategy for identifying a subset of potentially functional non-coding regulatory SNPs.
一类影响疾病易感性的重要基因变异可能存在于影响基因表达的调控元件中。调控序列难以识别，且可能与其调控的基因相距甚远，但许多调控序列位于进化保守区域（ECR）内。我们利用比较基因组学方法，在IGF1基因5'端上游达75 kb及内含子区域内鉴定出12个ECR。通过高分辨率熔解曲线分析对这些区域进行筛选，共鉴定出18个单核苷酸多态性（SNP），其中包括5个新变异。我们分析了两个基于大样本人群的健康女性系列，以检测ECR内次要等位基因频率（MAF）>1%的9个SNP。在多变量分析中，ECR内的9个SNP中有3个（rs35455143、rs35765817和rs3839984）与循环IGF1水平显著相关（每个SNP的P≤0.02，总体显著性P<0.001）。这3个SNP均为罕见SNP（MAF≤10%），位于IGF1基因5'端上游>70 kb处。其中两个（rs35455143和rs35765817）处于强连锁不平衡状态，且对循环IGF1水平似乎具有相反的影响。我们对IGF1基因内或附近其他SNP子集的研究结果与先前报道的与IGF1水平的关联一致，尽管只有一个（rs35767：P = 0.05）具有统计学显著性。我们认为，这是首次对与基因相邻的大片区域内ECR中的SNP与表型之间的关联进行系统研究。靶向ECR似乎是识别潜在功能性非编码调控SNP子集的一种有用策略。
